Category: Misc.

Overselling Genomics Award #2

Well, all I can say is “Aaaaargh” again. So I am awarding my second overselling genomics award to a Press Release from U. Florida entitled “Conquest of land began in shark genome” relating to a paper in PLoS One on shark development . The press release centers on a reported finding that

Using molecular markers to study the formation of skeletal cartilage in embryos of the spotted catshark, UF scientists isolated and tracked the activity of Hox genes, a group of genes that control how and where body parts develop in all animals, including people.

Now admittedly, this is not genomics here – but the press release just had to use genomics in the title so my automated google search for “genome” and “evolution” picked it up. So – why do they get the overselling award? Read more in the press release:

The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, shedding light on how life on Earth developed and potentially providing insight for scientists seeking ways to cure human birth defects, which affect about 150,000 infants annually in the United States.

Yes that is right, this genome-ish gene expression study in sharks is going to help cure human birth defects (note the paper in PLoS One seems entirely reasonable … this is another case of press releases being disconnected from the science – and is another reason to support OA publications because here you can actually all go and read the paper and ignore the press release).

In addition, the press release says

“We’ve uncovered a surprising degree of genetic complexity in place at an early point in the evolution of appendages,” said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. “Genetic processes were not simple in early aquatic vertebrates only to become more complex as the animals adapted to terrestrial living. They were complex from the outset. Some major evolutionary innovations, like digits at the end of limbs, may have been achieved by prolonging the activity of a genetic program that existed in a common ancestor of sharks and bony fishes.”

Now I accept that the specific details of Hox gene expression here might have been surprising but what friggin evolution textbook are these people reading if they are surprised that there is not a chain of life going from less complex to the pinnacle of complexity in humans? Hopefully not mine.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Check out Eye-On-DNAs Grand Rounds

Just a little post here suggesting people check out the Medical Blog Carnival Grand Rounds at Eye on DNA here.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Why all medical professionals need to study evolution

As an evolutionary biologist with a 50% appointment in a medical school (in the Med. Micro. and Immunology department at U. C. Davis – my other 50% is in the Section of Evolution and Ecology on the main campus) I am somewhat dismayed by the lack of attention evolution receives in Medical Schools.

So I am starting a new thread here on my blog about why medical professionals need to understand evolutionary biology. First, there is a great site out there for people who want to learn more called the “Evolution and Medicine Network” which has links to courses, articles, books, etc.

Here are my top 10 picks for reasons medical professional need to understand evolution

  1. Antibiotic resistance. The emergence and spread of antibiotic resistance is one of the most vexing issues in medicine right now as well as one of the best studied topics in the evolution of microorganisms. Understanding how antibiotic resistance originates and spreads is fundamentally a question of evolution. The more medical professionals understand this issue the better they will be at preventing spread in hospitals and in convincing patients and the community to stop abusing antibiotics in human and animal care.
  2. Origin and spread of virulence. Not all pathogens are equal. Some are minor annoyances. Others produce really nasty outcomes. And importantly, organisms can change these virulence properties on the short term. Even more importantly, behavior of medical personnel can both influence the spread of virulent strains (can anyone say – wash your *$&% hands) and can unintentionally select for more virulent strains. Understanding the evolution of virulence is critical for making sure health care does not make things worse (see papers by Ewald for example).
  3. Vaccine use and development. Vaccines involve altering the evolutionary arms race between pathogens and hosts. It is not an intelligent design arms race. If you do not get the difference, stay out of vaccine work.
  4. Cancer origins. Cancer is in essence a analog of natural selection operating among cells within the body. Unfortunately for us, the “winners” of this selection process are those that have uncontrolled growth. Thinking of cancer in this way can help understand how to both prevent and treat it.
  5. The human microbiome. Beneficial microbes are all over us and play fundamental roles in human health. Unfortunately they are very hard to study because, well, they are small, and many cannot be grown in culture in the lab. The current ways to study them primarily involve indirect DNA based assays involving evolutionary and ecological analyses of the data.
  6. Understanding the human genome. The human genome is done (well, almost, but close enough for most uses). Now what? Well, the best way to learn about the genome sequence itself is through “phylogenomic” analyses comparing to other genomes.
  7. The relevance of animal and other models. Mouse is a useful model for some aspects of human biology but not all. Drosophila too. And even yeast and E. coli? Which aspects of human biology can be modelled by each model organism? Understanding their evolutionary history and evolutionary processes helps figure this out.
  8. Aging. Aging is in essence an unfortunate side effect of natural selection maximizing fitness by futzing with health and reproduction in the early years. Since there is little fitness cost to mutations that lead to deleterious effects when we are old, well, we are kind of screwed. But understanding the ailments associated with aging is best done with this knowledge of the efficiencies and inefficiencies of selection.
  9. The immune system. See #3 above. But this is bigger than that. The whole process of how the immune system (both the innate and the adaptive components) works both at the level of an individual and at the level of a population is an exercise in population genetics and natural selection.
  10. Pluses and minuses of high mutation and recombination rates. Many medical professionals know HIV has a high mutation rate. And some might know that recombination rates are high in some pathogens. What are the consequences of this on the pathogen biology? Read Evolution 101, or my new textbook.
  11. A bonus one. Epidemiology of infectious diseases. One of the best tools in studying the spread of infectious diseases is phylogenetic analysis – which can show how different strains are related to each other.

Just a brief tour of some of the areas that evolutionary biology informs medicine. More on this later.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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The human genome war from a fun perspective

So I was browsing around Amazon because I have a new Evolution Textbook that just came out. And when I searched for “genomics” and “evolution” up popped a “Listmania” list (which I had never heard of before) for Books about J. Craig Venter. And then I saw a new book by Craig – his autobiography “A life decoded: my genome: my life” coming out in October. And that’s when I discovered that the people who bought his book (even though it has not come out yet) also bought

So people apparently link Craig to atheism and Einstein. So I said to myself – what about other books by the genome-war folks? What else did people buy when they bought them? This is where the fun began.

Francis Collins: The Language of God.

So apparently, Francis has the religious readers on his side but nobody seems to link him to science in much of any way.

John Sulston’s a Common Thread

So it seems Sulston has gotten all the people interested in science history.

Michael Ashburner’s Won for All

So I guess Ashburner gets the people interested in the science itself.

I am sure there is more fun to be had here with these. And as my brother pointed out – the Amazon function here of listing what other people bought does not say it is representative in any way (that is, they are trying to sell books so perhaps they list the most popular other books not the ones most commonly linked to the book in question). But it is kind of voyeuristic and fun to see the types of books people are buying in association with these books.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Metagenomics Based Discovery Highlight: Novel Photosynthetic Organism Discovered

Normally I avoid writing about discoveries in non Open Access journals. But I cannot help myself here. On Friday a wickedly cool paper was published in a journal that I will not name here. In this paper they describe a new bacterium: “Candidatus Chloracidobacterium thermophilum.” It is REALLY rare for a new bacteria to be described in a journal like this one. How did they get it in this journal? Well this organism represents the first new photosynthetic lineage of organisms discovered in many many many years. The bacterium is in the phylum Acidobacteria and can carry out aerobic photosynthesis. Prior to this discovery, photosynthesis was only known in five evolutionary lineages – all of them bacteria: Cyanobacteria, Chlorobi, Chloroflexi, Proteobacteria and Firmicutes. Photosynthesis in plants, algae and other eukaryotes all came from symbioses with cyanobacteria to these five groups represented the only “primary” photosynthetic lineages. Thus it is a big deal to find a sixth lineage having photosynthesis.

And – here is the fun part. How did they find this? With the help of metagenomics.

Only five bacterial phyla with members capable of chlorophyll (Chl)–based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)–synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. “Candidatus Chloracidobacterium thermophilum” is a BChl-producing member of the poorly characterized phylum Acidobacteria.

That is, they saw the first hints of this through analysis of metagenomic data which was generated by isolating DNA from a Yellowstone hot spring and sequencing the snot out of it. Anyway – as some might have guessed – my only lament about this paper is that it is in a non Open Access journal (I tried to convince the lead author to submit elsewhere but was not convincing enough I guess). It really is too bad – it would be nice to post some of their figures here for others to look at and it this paper would make a great one to use for educating the public about metagenomics. But alas the public cannot get this from Science for at least 1 year and bloggers and other news sources cannot really run with the story because of the copyright limitations. So – great science and great example of the power of metagenomics but restricted public use.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Science like the start of Apple?

I know a lot has been written in support of Open Access publishing and Open Science but I must say this paragraph (from MungBeing magazine by Andrew Hessel) is one of my favorites is more over the top than I initially realized,

Garage Biology and Open Source Biology: Twenty five years ago, kids flocked to computers, pushing the limits of what they could do. Similarly, the next generation of genetic engineers won’t need laboratories or even PhD: they’ll have laptops, cheap mail order DNA synthesis, and, thanks to Google and Wikipedia and open journals like PLOS Biology, access to mountains of free biological data. They’ll work in basements, garages, and cafes, and they’ll trade ideas and collaborate on genetic designs the same way open source programmers now write computer code. Keep in mind that it was only 30 years ago that a little company called Apple started out of a California garage.

Thanks to Bill Hooker’s blog response for calming me down a bit about how brilliant this quote is. The main issue I have is that there are risks associated with genome engineering that are different and more substantial than those associated with piecing together computers here and there.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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The pope is committed to evolution

Well, in my last post I asked if people were committed to “Evolution” and I confess I got a bit worried that this might be misinterpreted by some as “We believe in evolution regardless of the facts.” And in fact there was one flame-like comment posting that I deleted from the comments.

But now apparently the Pope has read my blog (or maybe someone told him about it) and he has come out in full support of evolution as a science and the facts of evolution as we evolutionary biologists know then (i.e., natural selection, macro and microevolution, etc).

As reported on MSNBC the Pope said

the debate raging in some countries —particularly the United States and his native Germany — between creationism and evolution was an “absurdity,” saying that evolution can coexist with faith.

In addition, he said

They are presented as alternatives that exclude each other,” the pope said. “This clash is an absurdity because on one hand there is much scientific proof in favor of evolution, which appears as a reality that we must see and which enriches our understanding of life and being as such.

Furthermore, and more importantly, the Pope has re-stated his belief that everyone must do something about global change and environmental destruction:

“We cannot simply do what we want with this Earth of ours, with what has been entrusted to us,” said the pope, who has been spending his time reading and walking in the scenic landscape bordering Austria.

I know I said recently that biology had a good day in the Bush administration. Unfortunately, that was mostly genetics and biochemistry. Evolution and environmental stewardship never seem to have good days there. Maybe just maybe, the Pope will have some impact around the world on both issues even as the U.S. sticks its head in the sand. NOTE – SEE COMMENTS – THE POPE IS PRETTY CLEARLY NOT DOING EVERYTHING HE COULD TO PROTECT THE ENVIRONMENT.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Are you committed to Evolution? Prove it!

Peggy Farnham at the U. C. Davis Genome Center sent me this picture. apparently of a real tattoo. After a google search I found at least an early source for it here.

This inspires me to ask everyone out there – are you committed to Evolution? What have you done to show your commitment?

What have I done? I think the biggest example of my commitment, though boring, is that I worked six years on a new evolution textbook which was just published a few weeks ago (which you can find out about here or order from Amazon here).

Less boring – I once stood on a street corner in New Orleans with Owen White and handed out altered forms of a pamphlet someone else was handing out in which we added some information about evolution.

So – rather that spout off about what I have done .. what has anyone else done? Are you committed?

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Single Cell Genomics Workshop at Bigelow Laboratory

Just got this email from Ramunas Stepanauskas regarding a workshop on single cell genomics. I had mentioned in my blog last week about how this seems to be a critical technology for the future of environmental microbiology. And if you want to get in early into this new technology — apply to this workshop.

I want to draw your attention to the workshop “Single Cell Alternatives to Metagenomics in Environmental Microbiology”, which will take place in Boothbay Harbor, Maine, during September 9-11:

We want to gather the different groups developing microbial single cell genomics (SCG) methodology, exchange information, and thereby enable the field to make faster progress; to examine the dominant science questions that are best addressed by this powerful new tool. The use of SCG will likely have a major impact on the fields of microbial ecology, evolution, and bioprospecting, by enabling partial or complete genome assembly of the uncultured taxa from complex communities, thus providing a critical link between isolate genomics and metagenomics. We envision workshop participants as a mix of about 30 principal investigators, graduate students, and postdocs.

Please see the website (above) for more information and how to apply.

Sincerely,
Ramunas Stepanauskas
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Rated my first paper in PLoS One

ResearchBlogging.org

Well, PLoS One has announced its rating system is open. See Chris Surridge’s Blog for more detail here. This is basically the first good system for trying out ratings for scientific publications in much the way it is done at YouTube and other Web 2.0 type systems.

I personally am not sure if I think PLoS One is the perfect system for scientific publishing. But we desperately need to try out new systems and as an Open Access Web 2.0 scientific publishing system, the concept is worth trying. So – I decided to try it.

I rated my first paper. I picked a paper by Xiang Xia Min and Donal Hickey on DNA barcoding. Why did I pick this paper. Well a few reasons. First, when I searched PLoS One for “metagenomics” and “metagenomic” it was one of the papers that came up. As soon as I saw the Barcoding title line I knew I had to look at this paper. Why? Well a few years ago, I posted a “dissent” on Faculty of 1000 about a paper on Barcoding. I stand by my dissent in that article. Basically I said that Barcoding sounded a heck of a lot like what Pace and others have been doing with rRNA surveying of uncultured microbes for a long long time. And it seems to me that the barcoding researchers are rediscovering some of the same findings and challenges that Pace and others found. Of course, not all can see my Faculty of 1000 review. Why? Well it is not Open Access. Bummer. Especially since the response by Hebert was unconvincing too … he basically said that rRNA was not used to delineate species. Apparently he had never heard of phylotypes or any of the extensive work using rRNA to do EXACTLY what they are suggesting mitochondrial genes could be used for in plants and animals.

Anyway – enough about Faculty of 1000. In the new paper, the authors discuss some aspects of barcoding and in particular they address whether one gene can represent all the genes in a mitochondrial genome. Basically, they say yes. But that is beside the point here. You want to know more. Read there paper here. And my comment here. That is yet another benefit of Open Access.

I call on everyone out there to find a paper in which you are interested and rate it and comment on it at PLoS One.

Min, X., & Hickey, D. (2007). DNA Barcodes Provide a Quick Preview of Mitochondrial Genome Composition PLoS ONE, 2 (3) DOI: 10.1371/journal.pone.0000325

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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